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DESCRIPTION

 Package: splatter
 Type: Package
 Title: Simple Simulation of Single-cell RNA Sequencing Data
-Version: 0.6.3
+Version: 0.6.4
 Date: 2016-10-13
 Author: Luke Zappia
 Authors@R: as.person(c(
@@ -25,7 +25,8 @@ Imports:
     locfit,
     akima,
     Biobase,
-    checkmate
+    checkmate,
+    methods
 Suggests:
     testthat
 biocViews: SingleCell, RNASeq, Transcriptomics, GeneExpression, Sequencing,

NAMESPACE

@@ -10,6 +10,7 @@ export(setParam)
 export(setParams)
 export(simpleSimulate)
 exportClasses(SimpleParams)
+importFrom(scater,newSCESet)
 importFrom(stats,median)
 importFrom(stats,rgamma)
 importFrom(stats,rnbinom)

R/params-functions.R

@@ -7,7 +7,7 @@
 #'
 #' @return List with the values of the selected parameters.
 #' @examples
-#' params <- simpleParams()
+#' params <- newSimpleParams()
 #' getParams(params, c("nGenes", "nCells", "mean.rate"))
 #' @export
 getParams <- function(params, names) {
@@ -37,7 +37,7 @@ getParams <- function(params, names) {
 #'
 #' @return Params object with updated values.
 #' @examples
-#' params <- simpleParams()
+#' params <- newSimpleParams()
 #' params
 #' # Set individually
 #' params <- setParams(params, nGenes = 1000, nCells = 50)

R/simple-estimate.R

@@ -2,8 +2,8 @@
 #'
 #' Estimate simulation parameters for the simple simulation from a real dataset.
 #'
-#' @param x either a counts matrix or an SCESet object containing count data to
-#'        estimate parameters from.
+#' @param data either a counts matrix or an SCESet object containing count data
+#'        to estimate parameters from.
 #' @param params SimpleParams object to store estimated values in.
 #'
 #' @details
@@ -24,14 +24,14 @@ estimateSimpleParams <- function(data, params = newSimpleParams()) {
     UseMethod("estimateSimpleParams")
 }
 
-#' @rdname simpleEstimate
+#' @rdname estimateSimpleParams
 #' @export
 estimateSimpleParams.SCESet <- function(data, params = newSimpleParams()) {
-    counts <- scater::counts(x)
+    counts <- scater::counts(data)
     estimateSimpleParams(counts, params)
 }
 
-#' @rdname simpleEstimate
+#' @rdname estimateSimpleParams
 #' @importFrom stats median
 #' @export
 estimateSimpleParams.matrix <- function(data, params = newSimpleParams()) {

R/simple-simulate.R

@@ -22,6 +22,7 @@
 #' sim <- simpleSimulate(nGenes = 1000, nCells = 50)
 #' @export
 #' @importFrom stats rgamma rnbinom
+#' @importFrom scater newSCESet
 simpleSimulate <- function(params = newSimpleParams(), verbose = TRUE, ...) {
 
     checkmate::assertClass(params, "SimpleParams")

man/estimateSimpleParams.Rd

@@ -2,15 +2,21 @@
 % Please edit documentation in R/simple-estimate.R
 \name{estimateSimpleParams}
 \alias{estimateSimpleParams}
+\alias{estimateSimpleParams.SCESet}
+\alias{estimateSimpleParams.matrix}
 \title{Estimate simple simulation parameters}
 \usage{
 estimateSimpleParams(data, params = newSimpleParams())
+
+\method{estimateSimpleParams}{SCESet}(data, params = newSimpleParams())
+
+\method{estimateSimpleParams}{matrix}(data, params = newSimpleParams())
 }
 \arguments{
-\item{params}{SimpleParams object to store estimated values in.}
+\item{data}{either a counts matrix or an SCESet object containing count data
+to estimate parameters from.}
 
-\item{x}{either a counts matrix or an SCESet object containing count data to
-estimate parameters from.}
+\item{params}{SimpleParams object to store estimated values in.}
 }
 \value{
 SimpleParams object containing the estimated parameters.

man/getParams.Rd

@@ -18,7 +18,7 @@ List with the values of the selected parameters.
 Get multiple parameter values from a Params object.
 }
 \examples{
-params <- simpleParams()
+params <- newSimpleParams()
 getParams(params, c("nGenes", "nCells", "mean.rate"))
 }
 

man/setParams.Rd

@@ -29,7 +29,7 @@ collecting parameter values in some way) or individually (useful when setting
 them manually), see examples.
 }
 \examples{
-params <- simpleParams()
+params <- newSimpleParams()
 params
 # Set individually
 params <- setParams(params, nGenes = 1000, nCells = 50)

man/simpleEstimate.Rd

-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/simple-estimate.R
-\name{estimateSimpleParams.SCESet}
-\alias{estimateSimpleParams.SCESet}
-\alias{estimateSimpleParams.matrix}
-\usage{
-\method{estimateSimpleParams}{SCESet}(data, params = newSimpleParams())
-
-\method{estimateSimpleParams}{matrix}(data, params = newSimpleParams())
-}
-

tests/testthat/test-simulate-simple.R

 context("simple simulation")
 
 test_that("simple simulation output is valid", {
-  expect_true(validObject(simSimple()))
+  expect_true(validObject(simpleSimulate()))
 })